# datamanager - easy access to and manipulation of data

The datamanager classes and functions are useful for locating the correct data file for a particular day and manipulating data and subsets in a generic way.

Authors: Jon Niehof

Institution: University of New Hampshire

Contact: Jonathan.Niehof@unh.edu

Copyright 2015

## About datamanager

## Examples

Examples go here

Classes

`DataManager`(directories, file_fmt[, ...]) | THIS CLASS IS NOT YET COMPLETE, doesn’t do much useful.

Functions

`apply_index`(data, idx) | Apply an array of indices to data.
`array_interleave`(array1, array2, idx) | Create an array containing all elements of both array1 and array2
`axis_index`(shape[, axis]) | Returns array of indices along axis, for all other axes
`flatten_idx`(idx[, axis]) | Convert multidimensional index into index on flattened array.
`insert_fill`(times, data[, fillval, tol, ...]) | Populate gaps in data with fill.
`rev_index`(idx[, axis]) | From an index, return an index that reverses the action of that index
`values_to_steps`(array[, axis]) | Transform values along an axis to their order in a unique sequence.

class `spacepy.datamanager.``DataManager`(directories, file_fmt, descend=False, period=None)

  THIS CLASS IS NOT YET COMPLETE, doesn’t do much useful.

  Will have to do something that allows the config file to specify regex and other things, and then just the directory to be changed (since regex, etc.

  Parameters: | directories : list A list of directories that might contain the data file_fmt : string Regular expression that matches the files desired. Will also recognize strftime parameters %w %d %m %y %Y %H %M %s %j %U %W, all zero-pad. https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior Can have subdirectory reference, but separator should be unix-style, with no leading slash. period : string Size of file; can be a number followed by one of d, m, y, H, M, s. Anything else is assumed to be “irregular” and files treated as if there are neither gaps nor overlaps in the sequence. If not specified, will be assumed to match one count of the smallest unit in the format string. Examples =======

  `files_matching`(dt=None)

    Return all the files matching this file format

    Parameters: | dt : datetime Optional; if specified, match only files for this date.
    Returns: | out : generator Iterates over every file matching the format specified at creation. Note this is specified in native path format!

  `get_filename`(dt)

    Returns the filename corresponding to a particular point in time

`spacepy.datamanager.``apply_index`(data, idx)

  Apply an array of indices to data.

  Most useful in dealing with the output from `numpy.argsort()`, and best explained by the example.

  Parameters: | data : array Input data, at least two dimensional. The 0th dimension is treated as a “time” or “record” dimension. idx : sequence 2D index to apply to the import data. The 0th dimension must be the same size as `data`‘s 0th dimension. Dimension 1 must be the same size as one other dimension in data (the first match found is used); this is referred to as the “index dimension.”
  Returns: | data : sequence View of `data`, with index applied. For each index of the 0th dimension, the values along the index dimension are obtained by applying the value of `idx` at the same index in the 0th dimension. This is repeated across any other dimensions in `data`. Warning No guarantee is made whether the returned data is a copy of the input data. Modifying values in the input may change the values of the input. Call `copy()` if a copy is required.
  Raises: | ValueError : if can’t match the shape of data and indices

  Examples

  Assume `flux` is a 3D array of fluxes, with a value for each of time, pitch angle, and energy. Assume energy is not necessarily constant in time, nor is ordered in the energy dimension. If `energy` is a 2D array of the energies as a function of energy step for each time, then the following will sort the flux at each time and pitch angle in energy order.

      >>> idx = numpy.argsort(energy, axis=1)
      >>> flux_sorted = spacepy.datamanager.apply_index(flux, idx)

`spacepy.datamanager.``array_interleave`(array1, array2, idx)

  Create an array containing all elements of both array1 and array2

  `idx` is an index on the output array which indicates which elements will be populated from `array1`, i.e., `out[idx] == array1` (in order.) The other elements of `out` will be filled, in order, from `array2`.

  Parameters: | array1 : array Input data. array2 : array Input data. Must have same number of dimensions as `array1`, and all dimensions except the zeroth must also have the same length. idx : array A 1D array of indices on the zeroth dimension of the output array. Must have the same length as the zeroth dimension of `array1`.
  Returns: | out : array All elements from `array1` and `array2`, interleaved according to `idx`.

  Examples

      >>> import numpy
      >>> import spacepy.datamanager
      >>> a = numpy.array([10, 20, 30])
      >>> b = numpy.array([1, 2])
      >>> idx = numpy.array([1, 2, 4])
      >>> spacepy.datamanager.array_interleave(a, b, idx)
      array([ 1, 10, 20,  2, 30])

`spacepy.datamanager.``axis_index`(shape, axis=-1)

  Returns array of indices along axis, for all other axes

  Parameters: | shape : tuple Shape of the output array
  Returns: | idx : array An array of indices. The value of each element is that element’s index along `axis`.
  Other Parameters:
  | axis : int Axis along which to return indices, defaults to the last axis.

  See also

  `numpy.mgrid`
    This function is a special case

  Examples

  For a shape of `(i, j, k, l)` and `axis` = -1, `idx[i, j, k, :] = range(l)` for all `i`, `j`, `k`.

  Similarly, for the same shape and `axis = 1`, `idx[i, :, k, l] = range(j)` for all `i`, `k`, `l`.

      >>> import numpy
      >>> import spacepy.datamanager
      >>> spacepy.datamanager.axis_index((5, 3))
      array([[0, 1, 2],
             [0, 1, 2],
             [0, 1, 2],
             [0, 1, 2],
             [0, 1, 2]])
      >>> spacepy.datamanager.axis_index((5, 3), 0)
          array([[0, 0, 0],
                 [1, 1, 1],
                 [2, 2, 2],
                 [3, 3, 3],
                 [4, 4, 4]])

`spacepy.datamanager.``flatten_idx`(idx, axis=-1)

  Convert multidimensional index into index on flattened array.

  Convert a multidimensional index, that is values along a particular axis, so that it can derefence the flattened array properly. Note this is not the same as `ravel_multi_index()`.

  Parameters: | idx : array Input index, i.e. a list of elements along a particular axis, in the style of `argsort()`.
  Returns: | flat : array A 1D array of indices suitable for indexing the flat version of the array
  Other Parameters:
  | axis : int Axis along which `idx` operates, defaults to the last axis.

  See also

  `apply_index`

  Examples

      >>> import numpy
      >>> import spacepy.datamanager
      >>> data = numpy.array([[3, 1, 2], [3, 2, 1]])
      >>> idx = numpy.argsort(data, -1)
      >>> idx_flat = spacepy.datamanager.flatten_idx(idx)
      >>> data.ravel() #flat array
      array([3, 1, 2, 3, 2, 1])
      >>> idx_flat #indices into the flat array
      array([1, 2, 0, 5, 4, 3])
      >>> data.ravel()[idx_flat] #index applied to the flat array
      array([1, 2, 3, 1, 2, 3])

`spacepy.datamanager.``insert_fill`(times, data, fillval=nan, tol=1.5, absolute=None, doTimes=True)

  Populate gaps in data with fill.

  Continuous data are often treated differently from discontinuous data, e.g., matplotlib will draw lines connecting data points but break the line at fill. Often data will be irregularly sampled but also contain large gaps that are not explicitly marked as fill. This function adds a single record of explicit fill to each gap, defined as places where the spacing between input times is a certain multiple of the median spacing.

  Parameters: | times : sequence Values representing when the data were taken. Must be one-dimensional, i.e., each value must be scalar. Not modified data : sequence Input data.
  Returns: | times, data : tuple of sequence Copies of input times and data, fill added in gaps (`doTimes` True) data : sequence Copy of input data, with fill added in gaps (`doTimes` False)
  Other Parameters:
  | fillval : Fill value, same type as `data`. Default is `numpy.nan`. If scalar, will be repeated to match the shape of `data` (minus the time axis). Note The default value of `nan` will not produce good results with integer input. tol : float Tolerance. A single fill value is inserted between adjacent values where the spacing in `times` is strictly greater than `tol` times the median of the spacing across all `times`. The inserted time for fill is halfway between the time on each side. (Default 1.5) absolute : An absolute value for maximum spacing, of a type that would result from a difference in `times`. If specified, `tol` is ignored and any gap strictly larger than `absolute` will have fill inserted. doTimes : boolean If True (default), will return a tuple of the times (with new values inserted for the fill records) and the data with new fill values. If False, will only return the data – useful for applying fill to multiple arrays of data on the same timebase.
  Raises: | ValueError : if can’t identify the time axis of data Try using `numpy.rollaxis()` to put the time axis first in both `data` and `times`.

  Examples

  This example shows simple hourly data with a gap, populated with fill. Note that only a single fill value is inserted, to break the sequence of valid data rather than trying to match the existing cadence.

      >>> import datetime
      >>> import numpy
      >>> import spacepy.datamanager
      >>> t = [datetime.datetime(2012, 1, 1, 0),
               datetime.datetime(2012, 1, 1, 1),
               datetime.datetime(2012, 1, 1, 2),
               datetime.datetime(2012, 1, 1, 5),
               datetime.datetime(2012, 1, 1, 6)]
      >>> temp = [30.0, 28, 27, 32, 35]
      >>> filled_t, filled_temp = spacepy.datamanager.insert_fill(t, temp)
      >>> filled_t
      array([datetime.datetime(2012, 1, 1, 0, 0),
             datetime.datetime(2012, 1, 1, 1, 0),
             datetime.datetime(2012, 1, 1, 2, 0),
             datetime.datetime(2012, 1, 1, 3, 30),
             datetime.datetime(2012, 1, 1, 5, 0),
             datetime.datetime(2012, 1, 1, 6, 0)], dtype=object)
      >>> filled_temp
      array([ 30.,  28.,  27.,  nan,  32.,  35.])

  This example plots “gappy” data with and without explicit fill values.

      >>> import matplotlib.pyplot as plt
      >>> import numpy
      >>> import spacepy.datamanager
      >>> x = numpy.append(numpy.arange(0, 6, 0.1), numpy.arange(12, 18, 0.1))
      >>> y = numpy.sin(x)
      >>> xf, yf = spacepy.datamanager.insert_fill(x, y)
      >>> fig = plt.figure()
      >>> ax0 = fig.add_subplot(211)
      >>> ax0.plot(x, y)
      >>> ax1 = fig.add_subplot(212)
      >>> ax1.plot(xf, yf)
      >>> plt.show()

  (Source code, png, hires.png, pdf)

`spacepy.datamanager.``rev_index`(idx, axis=-1)

  From an index, return an index that reverses the action of that index

  Essentially, `a[idx][rev_index(idx)] == a`

  Note

  This becomes more complicated in multiple dimensions, due to the vagaries of applying a multidimensional index.

  Parameters: | idx : array Indices onto an array, often the output of `argsort()`.
  Returns: | rev_idx : array Indices that, when applied to an array after `idx`, will return the original array (before the application of `idx`).
  Other Parameters:
  | axis : int Axis along which to return indices, defaults to the last axis.

  See also

  `apply_index`

  Examples

      >>> import numpy
      >>> import spacepy.datamanager
      >>> data = numpy.array([7, 2, 4, 6, 3])
      >>> idx = numpy.argsort(data)
      >>> data[idx] #sorted
      array([2, 3, 4, 6, 7])
      >>> data[idx][spacepy.datamanager.rev_index(idx)] #original
      array([7, 2, 4, 6, 3])

`spacepy.datamanager.``values_to_steps`(array, axis=-1)

  Transform values along an axis to their order in a unique sequence.

  Useful in, e.g., converting a list of energies to their steps.

  Parameters: | array : array Input data.
  Returns: | steps : array An array, the same size as `array`, with values along `axis` corresponding to the position of the value in `array` in a unique, sorted, set of the values in `array` along that axis. Differs from `argsort()` in that identical values will have identical step numbers in the output.
  Other Parameters:
  | axis : int Axis along which to find the steps.

  Examples

      >>> import numpy
      >>> import spacepy.datamanager
      >>> data = [[10., 12., 11., 9., 10., 12., 11., 9.],
                  [10., 12., 11., 9., 14., 16., 15., 13.]]
      >>> spacepy.datamanager.values_to_steps(data)
      array([[1, 3, 2, 0, 1, 3, 2, 0],
             [1, 3, 2, 0, 5, 7, 6, 4]])